1G9T

CRYSTAL STRUCTURE OF E.COLI HPRT-GMP COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase.

Guddat, L.W.Vos, S.Martin, J.L.Keough, D.T.de Jersey, J.

(2002) Protein Sci. 11: 1626-1638

  • DOI: 10.1110/ps.0201002
  • Primary Citation of Related Structures:  1G9S, 1GRV

  • PubMed Abstract: 
  • Crystal structures have been determined for free Escherichia coli hypoxanthine phosphoribosyltransferase (HPRT) (2.9 A resolution) and for the enzyme in complex with the reaction products, inosine 5'-monophosphate (IMP) and guanosine 5'-monophosphate ...

    Crystal structures have been determined for free Escherichia coli hypoxanthine phosphoribosyltransferase (HPRT) (2.9 A resolution) and for the enzyme in complex with the reaction products, inosine 5'-monophosphate (IMP) and guanosine 5'-monophosphate (GMP) (2.8 A resolution). Of the known 6-oxopurine phosphoribosyltransferase (PRTase) structures, E. coli HPRT is most similar in structure to that of Tritrichomonas foetus HGXPRT, with a rmsd for 150 Calpha atoms of 1.0 A. Comparison of the free and product bound structures shows that the side chain of Phe156 and the polypeptide backbone in this vicinity move to bind IMP or GMP. A nonproline cis peptide bond, also found in some other 6-oxopurine PRTases, is observed between Leu46 and Arg47 in both the free and complexed structures. For catalysis to occur, the 6-oxopurine PRTases have a requirement for divalent metal ion, usually Mg(2+) in vivo. In the free structure, a Mg(2+) is coordinated to the side chains of Glu103 and Asp104. This interaction may be important for stabilization of the enzyme before catalysis. E. coli HPRT is unique among the known 6-oxopurine PRTases in that it exhibits a marked preference for hypoxanthine as substrate over both xanthine and guanine. The structures suggest that its substrate specificity is due to the modes of binding of the bases. In E. coli HPRT, the carbonyl oxygen of Asp163 would likely form a hydrogen bond with the 2-exocyclic nitrogen of guanine (in the HPRT-guanine-PRib-PP-Mg(2+) complex). However, hypoxanthine does not have a 2-exocyclic atom and the HPRT-IMP structure suggests that hypoxanthine is likely to occupy a different position in the purine-binding pocket.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, School of Molecular and Microbial Science, The University of Queensland, St. Lucia, Qld. 4072, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE
A, B
182Escherichia coli (strain K12)Gene Names: hpt
EC: 2.4.2.8
Find proteins for P0A9M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A9M2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N
Query on N

Download SDF File 
Download CCD File 
B
ANY 5'-MONOPHOSPHATE NUCLEOTIDE
1-DEOXY-RIBOFURANOSE-5'-PHOSPHATE
C5 H11 O7 P
CYZZKTRFOOKUMT-LMVFSUKVSA-N
 Ligand Interaction
5GP
Query on 5GP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5GPKi: 526000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.199 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 84.140α = 90.00
b = 84.140β = 90.00
c = 167.270γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-08-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance